Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes

Journal of Proteome Research

Volumn 9, Issue 1, 2010, Pages 495-508

  Qattan, Amal T ^a   Mulvey, Claire ^a   Crawford, Mark ^a   Natale, Darren A ^b   Godovac Zimmermann, Jasminka ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Breast cancer; Mass spectrometry; MCF 7 cells; Quantitative proteomics; Subcellular location; Subcellular organelles

Indexed keywords

CELL PROTEIN;

ARTICLE; BREAST CANCER; CELL FRACTIONATION; CELL ORGANELLE; CELL STRAIN MCF 7; CELLULAR DISTRIBUTION; CONTROLLED STUDY; HUMAN; HUMAN CELL; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEOMICS; QUANTITATIVE ANALYSIS;

BREAST NEOPLASMS; CENTRIFUGATION, DENSITY GRADIENT; CLUSTER ANALYSIS; FEMALE; HUMANS; NEOPLASM PROTEINS; ORGANELLES; PROTEOMICS; SUBCELLULAR FRACTIONS; SUCROSE; TANDEM MASS SPECTROMETRY;

EID: 73649132649     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr9008332     Document Type: Article

References (32)

1. http://www.ncbi.nlm.nih.gov.
2. http://www.imaginis.com/breasthealth/statistics.asp#1.
3. Ince, T. A.; Weinberg, R. A. Functional genomics and the breast cancer problem. Cancer Cell 2002, 1, 15-17.
4. Van't Veer, L. J.; Dai, H.; van de Vijver, M. J.; He, Y. D.; Hart, A. A.; Mao, M.; Peterse, H. L.; van der, K. K.; Marton, M. J.; Witteveen, A. T.; Schreiber, G. J.; Kerkhoven, R. M.; Roberts, C.; Linsley, P. S.; Bernards, R.; Friend, S. H. A gene-expression signature as a predictor of survival in breast cancer. Nature 2002, 415, 530-536.
5. Sorlie, T.; Perou, C. M.; Tibshirani, R.; Aas, T.; Geisler, S.; Johnsen, H.; Hastie, T.; Eisen, M. B.; van de, R. M.; Jeffrey, S. S.; Thorsen, T.; Quist, H.; Matese, J. C.; Brown, P. O.; Botstein, D.; Eystein, L. P.; Borresen-Dale, A. L. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10869-10874.
6. Sebastian, T.; Johnson, P. F. Stop and go: anti-proliferative and mitogenic functions of the transcription factor C/EBPbeta. Cell Cycle 2006, 5, 953-957.
7. Hanahan, D.; Weinberg, R. A. The hallmarks of cancer. Cell 2000, 100, 57-70.
8. Roberts, G. C.; Smith, C. W. Alternative splicing: combinatorial output from the genome. Curr. Opin. Chem. Biol. 2002, 6, 375-383.
9. Godovac-Zimmermann, J.; Kleiner, O.; Brown, L. R.; Drukier, A. Perspectives in spicing up proteomics with splicing. Proteomics 2005, 5, 699-709.
10. Gygi, S. P.; Rochon, Y.; Franza, B. R. Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19, 1720-1730.
11. Lacroix, M.; Leclercq, G. Relevance of breast cancer cell lines as models for breast tumours: an update. Breast Cancer Res. Treat. 2004, 83, 249-89.
12. Soule, H. D.; Vazquez, J.; Long, A.; Albert, S.; Brenan, S. A human cell line from a pleural effusion derived from a breast carcinoma. J. Natl. Cancer Inst. 1973, 51, 1409-1413.
13. Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227, 680-685.
14. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 1996, 68, 850-858.
15. Usaite, R.; Wohlschlegel, J.; Venable, J. D.; Park, S. K.; Nielsen, J.; Olsson, L.; Yates III, J. R. Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods. J. Proteome Re.s 2008, 7, 266-275.
16. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
17. Kulasingam, V.; Diamandis, E. P. Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Mol. Cell. Proteomics 2007, 6, 1997-2011.
18. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
19. Florens, L.; Carozza, M. J.; Swanson, S. K.; Fournier, M.; Coleman, M. K.; Workman, J. L.; Washburn, M. P. Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 2006, 40, 303-311.
20. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
21. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
22. Dunkley, T. P.; Watson, R.; Griffin, J. L.; Dupree, P.; Lilley, K. S. Localization of organelle proteins by isotope tagging (LOPIT). Mol. Cell. Proteomics 2004, 3, 1128-1134.
23. Foster, L. J.; de Hoog, C. L.; Zhang, Y.; Zhang, Y.; Xie, X.; Mootha, V. K.; Mann, M. A mammalian organelle map by protein correlation profiling. Cell 2006, 125, 187-199.
24. Simpson, J. C.; Pepperkok, R. The subcellular localization of the mammalian proteome comes a fraction closer. Genome Biol. 2006, 222.
25. Yates, J. R., 3rd.; Gilchrist, A.; Howell, K. E.; Bergeron, J. J. Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell. Biol. 2005, 6, 702-714.
26. Au, C. E.; Bell, A. W.; Gilchrist, A.; Hiding, J.; Nilsson, T.; Bergeron, J. J. Organellar proteomics to create the cell map. Curr. Opin. Cell Biol. 2007, 19, 376-385.
27. Rogers, L. D.; Foster, L. J. The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18520-18525.
28. Xu, P.; Crawford, M.; Way, M.; Godovac-Zimmermann, J.; Segal, A.; Radulovic, M. Subproteome analysis of the neutrophil cytoskeleton. Proteomics 2009, 9, 2037-2049.
29. Sorokin, A. V.; Kim, E. R.; Ovchinnikov, L. P. Nucleocytoplasmic transport of proteins. Biochemistry (Mosc). 2007, 72, 1439-1457.
30. Andersen, J. S.; Lam, Y. W.; Leung, A. K.; Ong, S. E.; Lyon, C. E.; Lamond, A. I.; Mann, M. Nucleolar proteome dynamics. Nature 2005, 433, 77-83.
31. Dundr, M.; Misteli, T. Nucleolomics: an inventory of the nucleolus. Mol. Cell 2002, 9, 5-7.
32. www.ncbi.nlm.nih.gov, www.uniprot.org, http://locate.imb.uq.edu.au accessed August 2009.